2B5L

Crystal Structure of DDB1 In Complex with Simian Virus 5 V Protein

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d2b5la3	All alpha proteins	DDB1 C-terminal-like	DDB1 C-terminal-like	DDB1 C-terminal-like	DDB1 C-terminal domain	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d2b5la1	All beta proteins	7-bladed beta-propeller	WD40 repeat-like	DDB1-like	DDB1	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d2b5lb3	All alpha proteins	DDB1 C-terminal-like	DDB1 C-terminal-like	DDB1 C-terminal-like	DDB1 C-terminal domain	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d2b5lb1	All beta proteins	7-bladed beta-propeller	WD40 repeat-like	DDB1-like	DDB1	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C	d2b5lc_	Alpha and beta proteins (a+b)	SV5-V core-like	SV5-V core-like	SV5-V core-like	SV5-V core	(Mammalian orthorubulavirus 5 ) [TaxId: 2560580 ],	SCOPe (2.08)
D	d2b5ld_	Alpha and beta proteins (a+b)	SV5-V core-like	SV5-V core-like	SV5-V core-like	SV5-V core	(Mammalian orthorubulavirus 5 ) [TaxId: 2560580 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	DDB1-like	8044839	4004169	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	WD40 repeat-like	8052530	3001694	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	WD40 repeat-like	8051194	3001694	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	WD40 repeat-like	8052531	3001694	SCOP2 (2022-06-29)
B	SCOP2B Superfamily	WD40 repeat-like	8051194	3001694	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	WD40 repeat-like	8052530	3001694	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	WD40 repeat-like	8052531	3001694	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	WD40 repeat-like	8052530	3001694	SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	CPSF_A_N	e2b5lA6	A: beta duplicates or obligate multimers	X: beta-propeller-like	H: beta-propeller	T: 7-bladed	F: CPSF_A_N	ECOD (1.6)
A	MMS1_N_C	e2b5lA7	A: beta duplicates or obligate multimers	X: beta-propeller-like	H: beta-propeller	T: 7-bladed	F: MMS1_N_C	ECOD (1.6)
A	MMS1_N_N	e2b5lA8	A: beta duplicates or obligate multimers	X: beta-propeller-like	H: beta-propeller	T: 7-bladed	F: MMS1_N_N	ECOD (1.6)
A	CPSF_A_C	e2b5lA1	A: alpha arrays	X: HTH	H: HTH	T: tri-helical	F: CPSF_A_C	ECOD (1.6)
B	CPSF_A_N	e2b5lB5	A: beta duplicates or obligate multimers	X: beta-propeller-like	H: beta-propeller	T: 7-bladed	F: CPSF_A_N	ECOD (1.6)
B	MMS1_N_C	e2b5lB6	A: beta duplicates or obligate multimers	X: beta-propeller-like	H: beta-propeller	T: 7-bladed	F: MMS1_N_C	ECOD (1.6)
B	MMS1_N_N	e2b5lB7	A: beta duplicates or obligate multimers	X: beta-propeller-like	H: beta-propeller	T: 7-bladed	F: MMS1_N_N	ECOD (1.6)
B	CPSF_A_C	e2b5lB1	A: alpha arrays	X: HTH	H: HTH	T: tri-helical	F: CPSF_A_C	ECOD (1.6)
C	zf-Paramyx-P	e2b5lC1	A: a+b three layers	X: Nonstructural protein V (From Topology)	H: Nonstructural protein V (From Topology)	T: Nonstructural protein V	F: zf-Paramyx-P	ECOD (1.6)
D	zf-Paramyx-P	e2b5lD1	A: a+b three layers	X: Nonstructural protein V (From Topology)	H: Nonstructural protein V (From Topology)	T: Nonstructural protein V	F: zf-Paramyx-P	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	2.130.10.10	Mainly Beta	7 Propeller	Methylamine Dehydrogenase	Chain H	CATH (4.3.0)
A	1.10.150.910	Mainly Alpha	Orthogonal Bundle	DNA polymerase	domain 1	CATH (4.3.0)
B	2.130.10.10	Mainly Beta	7 Propeller	Methylamine Dehydrogenase	Chain H	CATH (4.3.0)
B	1.10.150.910	Mainly Alpha	Orthogonal Bundle	DNA polymerase	domain 1	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF10433	RSE1/DDB1/CPSF1 first beta-propeller (Beta-prop_RSE1_1st)	Mono-functional DNA-alkylating methyl methanesulfonate N-term	-	Repeat
A, B	PF03178	CPSF A subunit region (CPSF_A)	CPSF A subunit region	-	Repeat
C, D	PF13008	Zinc-binding domain of Paramyxoviridae V protein (zf-Paramyx-P)	Zinc-binding domain of Paramyxoviridae V protein	The Paramyxoviridae, which include such respiroviruses as para-influenzae and measles, produce phosphoproteins - protein P - that are integral to the polymerase transcription-replication complex. Protein P consists of two functionally distinct moieti ...	The Paramyxoviridae, which include such respiroviruses as para-influenzae and measles, produce phosphoproteins - protein P - that are integral to the polymerase transcription-replication complex. Protein P consists of two functionally distinct moieties, an N-terminal PNT, and a C-terminal PCT [1]. The P gene region transcribes proteins from all three ORFs, and the V protein consists of the PNT moiety and a more C-terminal 2-zinc-binding domain. This conserved region consists of the two-zinc-binding section sandwiched between beta sheets 6 and 7 of the overall V protein. It is the binding of this core domain of V protein with the DDB1 protein (part of the ubiquitin-ligase complex) of eukaryotes which represents the key element of the virus-host protein interaction [3]. In the Henipavirus family which includes Nipah and Hendra viruses, the V protein is able to block IFN (interferon) signalling by preventing IFN-induced STAT phosphorylation and nuclear translocation [2]. The P gene of morbillivirus is co-transcriptionally edited leading to a V protein being produced.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	damage-specific DNA binding protein 1	ubiquitin ligase complex scaffold activity protein-macromolecule adaptor activity molecular adaptor activity DNA binding binding organic cyclic compound binding nucleic acid binding protein-containing complex binding protein binding cullin family protein binding damaged DNA binding WD40-repeat domain binding protein domain specific binding	cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular process catabolic process proteolysis involved in protein catabolic process proteasomal protein catabolic process primary metabolic process protein catabolic process macromolecule catabolic process proteolysis metabolic process cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular process catabolic process proteolysis involved in protein catabolic process proteasomal protein catabolic process primary metabolic process protein catabolic process macromolecule catabolic process proteolysis metabolic process protein metabolic process macromolecule metabolic process apoptotic process cell death programmed cell death protein ubiquitination macromolecule modification post-translational protein modification protein modification process protein modification by small protein conjugation protein modification by small protein conjugation or removal regulation of biological process negative regulation of reproductive process regulation of reproductive process reproductive process biological regulation negative regulation of biological process modification-dependent macromolecule catabolic process modification-dependent protein catabolic process ubiquitin-dependent protein catabolic process regulation of biosynthetic process epigenetic programming of gene expression regulation of cellular process epigenetic programming in the zygotic pronuclei epigenetic regulation of gene expression regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process cellular component organization regulation of gene expression biosynthetic process chromatin organization chromatin remodeling regulation of macromolecule biosynthetic process cellular component organization or biogenesis regulation of metabolic process regulation of cell cycle phase transition regulation of cell cycle process cell cycle phase transition mitotic cell cycle regulation of mitotic cell cycle phase transition regulation of mitotic cell cycle mitotic cell cycle process cell cycle regulation of cell cycle mitotic cell cycle phase transition cell cycle process DNA metabolic process nucleic acid metabolic process nucleobase-containing compound metabolic process DNA repair positive regulation of viral genome replication positive regulation of viral process positive regulation of biological process viral life cycle regulation of viral process regulation of viral life cycle viral genome replication viral process regulation of viral genome replication developmental process cellular developmental process cell development developmental process involved in reproduction programmed cell death involved in cell development cell differentiation anatomical structure development ectopic germ cell programmed cell death nucleotide-excision repair response to light stimulus cellular response to environmental stimulus cellular response to light stimulus cellular response to radiation response to UV UV-damage excision repair response to radiation response to abiotic stimulus cellular response to abiotic stimulus cellular response to UV monosaccharide metabolic process gluconeogenesis regulation of primary metabolic process positive regulation of metabolic process regulation of small molecule metabolic process positive regulation of biosynthetic process small molecule metabolic process regulation of carbohydrate metabolic process regulation of glucose metabolic process positive regulation of cellular process positive regulation of gluconeogenesis carbohydrate metabolic process small molecule biosynthetic process carbohydrate biosynthetic process hexose metabolic process monosaccharide biosynthetic process hexose biosynthetic process positive regulation of glucose metabolic process regulation of gluconeogenesis positive regulation of carbohydrate metabolic process regulation of carbohydrate biosynthetic process positive regulation of small molecule metabolic process glucose metabolic process rhythmic process circadian rhythm regulation of circadian rhythm negative regulation of programmed cell death regulation of apoptotic process regulation of programmed cell death negative regulation of apoptotic process negative regulation of cellular process positive regulation of protein metabolic process positive regulation of macromolecule metabolic process regulation of protein metabolic process regulation of catabolic process positive regulation of protein catabolic process positive regulation of catabolic process regulation of protein catabolic process biological process involved in interspecies interaction between organisms biological process involved in interaction with symbiont biological process involved in symbiotic interaction regulation by virus of viral protein levels in host cell positive regulation by virus of viral protein levels in host cell regulation of biological quality proteasome-mediated ubiquitin-dependent protein catabolic process regulation of developmental process negative regulation of developmental process exit from host cell viral release from host cell biological process involved in interaction with host meiotic chromosome segregation sexual reproduction microtubule cytoskeleton organization membraneless organelle assembly female gamete generation meiotic cell cycle process gamete generation cellular component biogenesis cellular component assembly female meiotic nuclear division meiotic nuclear division chromosome segregation spindle organization organelle assembly organelle fission meiotic cell cycle multicellular organismal reproductive process meiotic spindle organization meiotic spindle assembly spindle assembly nuclear division organelle organization nuclear chromosome segregation microtubule-based process cytoskeleton organization spindle assembly involved in female meiosis cell surface receptor signaling pathway signaling cell communication signal transduction Wnt signaling pathway	extracellular exosome membrane-bounded organelle extracellular vesicle cellular anatomical structure extracellular organelle extracellular region organelle extracellular space vesicle extracellular membrane-bounded organelle intracellular anatomical structure cytoplasm intracellular organelle membraneless organelle extracellular exosome membrane-bounded organelle extracellular vesicle cellular anatomical structure extracellular organelle extracellular region organelle extracellular space vesicle extracellular membrane-bounded organelle intracellular anatomical structure cytoplasm intracellular organelle membraneless organelle intracellular membraneless organelle chromosome chromosome, telomeric region chromosomal region nucleus membrane-enclosed lumen intracellular membrane-bounded organelle nucleolus intracellular organelle lumen organelle lumen nuclear lumen cullin-RING ubiquitin ligase complex protein-containing complex ubiquitin ligase complex catalytic complex Cul4-RING E3 ubiquitin ligase complex transferase complex intracellular protein-containing complex Cul4A-RING E3 ubiquitin ligase complex nucleoplasm site of double-strand break site of DNA damage Cul4B-RING E3 ubiquitin ligase complex
C, D	Nonstructural protein V	ubiquitin-like ligase-substrate adaptor activity enzyme-substrate adaptor activity protein-macromolecule adaptor activity molecular adaptor activity RNA binding binding organic cyclic compound binding nucleic acid binding cation binding ion binding metal ion binding small molecule binding	symbiont-mediated perturbation of host defense response biological process involved in interspecies interaction between organisms symbiont-mediated perturbation of host process viral process modulation by virus of host process virus-mediated perturbation of host defense response modulation of process of another organism biological process involved in interaction with host modulation by virus of host cellular process biological process involved in symbiotic interaction symbiont-mediated suppression of host signal transduction pathway symbiont-mediated perturbation of host cellular process symbiont-mediated suppression of host interferon-mediated signaling pathway symbiont-mediated suppression of host type I interferon-mediated signaling pathway symbiont-mediated perturbation of host defense response biological process involved in interspecies interaction between organisms symbiont-mediated perturbation of host process viral process modulation by virus of host process virus-mediated perturbation of host defense response modulation of process of another organism biological process involved in interaction with host modulation by virus of host cellular process biological process involved in symbiotic interaction symbiont-mediated suppression of host signal transduction pathway symbiont-mediated perturbation of host cellular process symbiont-mediated suppression of host interferon-mediated signaling pathway symbiont-mediated suppression of host type I interferon-mediated signaling pathway symbiont-mediated perturbation of host signal transduction pathway response to stimulus symbiont-mediated suppression of host pathogen-associated molecular pattern receptor signaling pathway symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MDA-5 activity response to biotic stimulus symbiont-mediated suppression of host immune response symbiont-mediated suppression of host innate immune response symbiont-mediated suppression of host defenses symbiont-mediated perturbation of host innate immune response response to host response to external biotic stimulus response to host defenses response to other organism symbiont-mediated perturbation of host immune response symbiont-mediated perturbation of host defenses response to defenses of other organism response to external stimulus symbiont-mediated suppression of cytoplasmic pattern recognition receptor signaling pathway symbiont-mediated suppression of host JAK-STAT cascade symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT activity symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT1 activity	host cellular component host intracellular part cellular anatomical structure host cell cytoplasm host cell part host intracellular region

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR018846	RSE1/DDB1/CPSF1, first beta-propeller domain	Domain
A, B	IPR036322	WD40-repeat-containing domain superfamily	Homologous Superfamily
A, B	IPR015943	WD40/YVTN repeat-like-containing domain superfamily	Homologous Superfamily
A, B	IPR004871	Cleavage/polyadenylation specificity factor, A subunit, C-terminal	Domain
A, B	IPR050358	RSE1/DDB1/CFT1/CPSF1	Family
C, D	IPR025909	Phosphoprotein P soyouz module	Domain
C, D	IPR024279	Paramyxovirinae protein V, zinc-binding domain	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B	Pharos: Q16531	Disease Exacerbation gastric cancer lung cancer xeroderma pigmentosum gastric neoplasm drug-induced liver injury hereditary diffuse gastric adenocarcinoma psoriasis

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.